I would expect to find out what the problem is on the other side of Northgate in Destiny's Conflict. The dragons being one of the main instigator's of conflict on Athera, I would be expecting to learn a bit more about them, and perhaps have them redeem themselves for their past actions. The young dragon's visit could have just been a forwarning of rebellion on the far side keeping the older dragons busy.
I still do not see Arithon ever accepting kingship, although there are different kinds of kingship other than earthly ones, he might not object to them all. Kingship of part of Athera, comes with Fellowship sanctioned power and attunements to all four elements. I am expecting Arithon to claim the elemental attunements for all of Athera, and not from Asandir or any other Fellowship source. So no strings attached requiring kingship, no need for any royal jewels, and he will not have gained power under the compact, so no ties to the Fellowship. Arithon's term of duty as Rathain's last Prince should only go for a lifetime, he dies presumably the Fellowship loose all claim on him, although Athera does not.
Daviens plans for Arithon did not seem to include kingship, although he acknowledged Arithon could do it either way. If Arithon has to choose between being king and having the Paravians return, or something that lets humanity develop without sacrificing his freedom to kingship, but also without a Paravian presence, what would he choose? Kingship was killing Athera's talent off almost as fast as the rebellion, and humans are not made to withstand Paravian presence long term. The compact created the split in the first place between the clans and the towns people. The clans had to keep their bloodlines pure to ensure they could uphold their part of the compact, and the towns people eventually lost any connection they had to the mysteries. I think Arithon would choose what was best for humanity over what he would want personally. So I am not getting my hopes up the Paravians will be returning to Paravia.
Once Arithon has the power of a king (with regards to the mysteries and Athera), and settled his future Davien should be happy and the Fellowship reunited, whether any actual black roses make an appearance on Daon Ramon remains to be seen. I am sort of expecting to find out the black rose is Athera and Arithon joined as one, but Janny is keeping us guessing. The Paravians are still going to have to put in an appearance when it comes time to sort out what everyone is going to be doing, and whether or not the compact between the Fellowship and the Paravians will continue. Presumably we get to that point after all the conflicts are resolved, which will hopefully be at the end of Destiny's Conflict.
I want Song of the Mysteries to be concentrating more on the Mysteries, if we get to go through some of the same conflicts I want to see what was happening behind the scenes, the mystery of the so far virtually unseen contributors to the story. How it all came about, where it all leads to, and all the mysteries in between, if Janny can fit it all in one book.
As to threads from CotM there are plenty, although I have not read the first book for a while here are a few ideas of what we still have left.
Conflict between Arithon and Lysaer, end of Desh-Thiere's curse and redemption of Lysaer
Mystery of what the Paravians are and where they went.
Conflict between the Fellowship and the Koriani
The Black Rose prophecy and the reuniting and restoration of the Fellowship
Davien's hidden agenda and why he split from the other six in the first place. Just why he built the fountain, Kewar, the shaft at Rockfell and all those stairs.
The rebellion and how that split is going to be resolved.
The missing Ciladis, and what it takes to wake him.
Traithe's restoration back to his full powers.
The wraiths at Rockfell cannot stay imprisoned forever.
The Fellowship are bound by the compact as well as their called duty to eradicate the drakespawn. Is there an actual end to those burdens.
Not all the dragon's creations have been redeemed yet.
The dragons seem to have created a bit of a bad reputation marring Ath's creation, can they make amends for those past mistakes?
The destruction of the original human civilisation, which brought humanity to Athera in the first place. What really caused it, what can be done to heal that damage.
The enslaved Koriani, and Elaira's destiny.
The mystery of the destiny of the clans and how kingship ties into that. How does a kingdom's loss of it's royal line mean that clan destiny is also lost. Not that I think any will actually miss out.
Elshian, Masterbards and two lyranthe's, there is bound to be a story there we get eventually. Probably the last book though.
Alithiel, her making and the other 11 Isaervian swords, a certain cinder of a fallen star. 12 Paravian lines, 12 lanes. And later we found out there were 12 mariner's stars, and Tysan's royal sigil was a 12 point gold star. Alithiel was a mystery by herself, but there might be even more too it. By the 11th book we should get that story. If we end up with 12 books I will not complain.
Just who were Elaira's parents and what happened to them.
Lirenda has waited so long, does she ever get her chance at prime power.
Morriel started not too bad and slowly descended just about as far as she could go. Is such perseverance to duty at the cost of everything going to be worth it. Is Morriel going to get her chance for redemption?
Way back in the first book a question was raised when Asandir was attempting to heal Arithon of the curse of Mearth. "This Prince could not be other than mortal" yet that was not the only time Arithon did not react as expected when called with compassion. And there have been other hints, especially in Initiate's Trial, where Janny has been more obvious. I doubt Janny will give away too many mysteries till the final book, but the hints should be getting a bit broader. I should think after Destiny's Conflict, some might start to speculate in that direction a bit more.
Humanity were only allowed to settle on Athera under the terms of the compact, so what happens when they eventually break the compact? We are probably going to find out in the next book. The conflict everyone knew was destined to happen.